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Published online before print July 2, 2008, 10.1110/ps.035899.108
Protein Science (2008), 17:1781-1790. Published by Cold Spring Harbor Laboratory Press. Copyright © 2008 The Protein Society
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Crystal structure of RimI from Salmonella typhimurium LT2, the GNAT responsible for N{alpha}-acetylation of ribosomal protein S18

Matthew W. Vetting, David C. Bareich, Michael Yu, and John S. Blanchard

Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, USA

(RECEIVED April 17, 2008; FINAL REVISION June 20, 2008; ACCEPTED June 20, 2008)

The three ribosomal proteins L7, S5, and S18 are included in the rare subset of prokaryotic proteins that are known to be N{alpha}-acetylated. The GCN5-related N-acetyltransferase (GNAT) protein RimI, responsible for the N{alpha}-acetylation of the ribosomal protein S18, was cloned from Salmonella typhimurium LT2 (RimIST), overexpressed, and purified to homogeneity. Steady-state kinetic parameters for RimIST were determined for AcCoA and a peptide substrate consisting of the first six amino acids of the target protein S18. The crystal structure of RimIST was determined in complex with CoA, AcCoA, and a CoA-S-acetyl-ARYFRR bisubstrate inhibitor. The structures are consistent with a direct nucleophilic addition–elimination mechanism with Glu103 and Tyr115 acting as the catalytic base and acid, respectively. The RimIST-bisubstrate complex suggests that several residues change conformation upon interacting with the N terminus of S18, including Glu103, the proposed active site base, facilitating proton exchange and catalysis.

Keywords: protein N{alpha}-acetylation; bisubstrate inhibition; GNAT structure; ribosomal protein


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